Hi Jesse, Your suggestions are being considered, but in the meantime, one of our developers offered these comments:
It's possible (though not convenient) to add an RGB tag to each line of BAM to get per-item colors. See "Use R,G,B colors specified in user-defined tag" in http://genome.ucsc.edu/goldenPath/help/hgBamTrackHelp.html. That would require some disk space and time depending on the size of the BAM files, but it's conceptually simple: 1. convert BAM to SAM 2. feed SAM to script that looks at the strand bit in the flag column and appends YC:Z:<rgb triplet> tag 3. convert modified SAM to BAM, index the new BAM -- Brooke Rhead UCSC Genome Bioinformatics Group On 07/22/11 21:58, Jesse Rodriguez wrote: > Hi Katrina, > > Thanks for passing this along and for the info -- I saw the bam > visualization options, but none of the combinations yielded any easy way to > see both strand info and variants. > > Jesse > > On Fri, Jul 22, 2011 at 5:49 PM, Katrina Learned <[email protected]>wrote: > >> Hi Jesse, >> >> Thank you for your feedback. I will pass this suggestion on to management >> for consideration. >> >> You can change the coloring of the alignments from the track controls page >> of your track, which you can get to by right-clicking on the track and >> selecting one of the configure options. Here is some information about the >> coloring options: >> http://genome.ucsc.edu/**goldenPath/help/**hgBamTrackHelp.html<http://genome.ucsc.edu/goldenPath/help/hgBamTrackHelp.html> >> >> Please contact the mail list ([email protected]) again if you have any >> further questions. >> >> Katrina Learned >> UCSC Genome Bioinformatics Group >> >> Jesse Rodriguez wrote, On 07/22/11 12:56: >> >>> Hello, >>> >>> Just as some feedback, I think the default forward/reverse coloring of the >>> bam reads makes it very difficult to spot mismatches in the reads. This >>> is >>> made worse by the fact that the mismatches are only one pixel wide instead >>> of being an entire base in width. It would be nice if the forward/reverse >>> coloring could be customized at the very least since lighter colors would >>> make the red of the mismatches stand out more, even if they weren't made 1 >>> base wide. >>> >>> Jesse Rodriguez >>> >>> PhD Candidate >>> Biomedical Informatics Program >>> Stanford University >>> ______________________________**_________________ >>> Genome maillist - [email protected] >>> https://lists.soe.ucsc.edu/**mailman/listinfo/genome<https://lists.soe.ucsc.edu/mailman/listinfo/genome> >>> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
